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:: Software ::

iBrain™, the iBrain™ Analysis Toolbox for SPM,
and the iBrain™ Laterality Toolbox

Principal developer: David Abbott, PhD
Co-developers: Richard Masterton, PhD; Tony Waites, PhD; Kaushik Bhaganagarapu; Gaby Pell, PhD; Matt Harvey; Gagan Sharma; Chris Tailby, PhD; Graeme Jackson, MD.

iBrain™ software comprises several easy-to-use neuroimage processing and visualisation packages developed by David Abbott PhD and his team. Please see the iBrain software page for more details.


MRtrix: MR tractography including crossing fibres
Principal Developer: Donald Tournier, PhD
Co-developers: David Raffelt, PhD; Robert Smith, PhD; Ben Jeurissen, PhD

MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.

MRtrix is released under the GNU General Public License. The stable 0.2 version is available for download at NITRC. Documentation for this version is available here. Note that this version is no longer under active development and now only receives bug fix updates.

The new MRtrix3 release, which includes the latest developments, is available on the MRtrix3 GitHub page, along with its documentation. While this version isn't yet an official release, it is already very stable. However, note that it is under active development, and as such subject to frequent changes.


NFG: The Numerical Fibre Generator

NFG: The 'Numerical Fibre Generator'
Version: 1.11
Developer: Tom Close

NFG is a collection of command-line tools that enable the generation of numerical fibre structures with a range of complexities spanning the levels expected of human white matter. Also included is a tool to simulate the diffusion-weighted MR (DW-MR) images that would arise from these structures under various imaging conditions. The primary use of the 'Numerical Fibre Generator' is to enable the testing of white-matter fibre tracking techniques based on DW-MRI.

All included tools are distributed under the GNU public licence (GPL) and are available for download at NITRC


Version: 1.0
Developer: Kaushik Bhaganagarapu

SOCK (Spatially Organized Component Klassifikator) can be used to automatically identify a high proportion of the artifactual components arising in Independent Componenets Analysis (ICA) of fMRI. It is described in detail in the following manuscript:

Bhaganagarapu K, Jackson GD, Abbott DF. An automated method for identifying artifact in Independent Component Analysis of resting-state fMRI. Frontiers in Human Neuroscience 7(343):1-16 (2013). (doi: 10.3389/fnhum.2013.00343).

The SOCK software is written in Matlab and presently works well with MELODIC ICA software (part of FSL from FMRIB).

SOCK software is released under the GNU General Public License, and is now available for download at NITRC.






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